3N77 | pdb_00003n77

Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2

• PDB DOI: https://doi.org/10.2210/pdb3N77/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-05-26 Released: 2010-08-18 
• Deposition Author(s): Frydrysiak, J., Cooper, D.R., Derewenda, U., Anderson, W.F., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI), Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2

Frydrysiak, J., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.83 kDa 
• Atom Count: 2,490 
• Modeled Residue Count: 282 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside triphosphatase nudI	A, B	144	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 4  Gene Names: nudI, STM2295, yfaO EC: 3.6.1 (PDB Primary Data), 3.6.1.12 (UniProt), 3.6.1.23 (UniProt), 3.6.1.9 (UniProt)
UniProt
Find proteins for Q8ZNF5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNF5  Go to UniProtKB:  Q8ZNF5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.498	α = 90
b = 66.268	β = 113.87
c = 50.836	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Frydrysiak, J., Cooper, D.R., Derewenda, U., Anderson, W.F., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI), Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description